def test_progress_log():
"""test_progress_log: simple test, just to make sure it is runnable
"""
traj = pt.datafiles.load_tz2()[:10]
p = ProgressBarTrajectory(traj, style='basic', every=5)
pt.molsurf(p)
p = ProgressBarTrajectory(traj, style='bar', every=5)
pt.molsurf(p)
p = ProgressBarTrajectory(traj, style='circle', every=5)
pt.molsurf(p)
# need to run on Jupyter notebook
if tqdm is not None:
p = ProgressBarTrajectory(traj, style='tqdm')
pt.molsurf(p)
try:
p = ProgressBarTrajectory(traj, style=tqdm_notebook)
pt.molsurf(p)
except traitlets.traitlets.TraitError:
pass
# make sure not loading all coordinates from TrajectoryIterator
traj2 = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
traj2._size_limit_in_GB = traj2._estimated_GB - 0.001
with pytest.raises(MemoryError):
traj2.xyz
p2 = ProgressBarTrajectory(traj2)
aa_eq(pt.rmsd(p2), pt.rmsd(traj2))
def test():
fname = 'data/nogit/remd/remd.x.000'
topname = 'data/nogit/remd/myparm.parm7'
traj = pt.trajectory.Trajectory(fname, top=topname)
print(traj.xyz.dtype)
for f in traj:
pass
pt.radgyr(traj)
pt.molsurf(traj, '@CA')
pt.rmsd(traj, mask='@CA')
pt.multidihedral(traj)
def test_2(traj=traj):
data = []
for idx, c in enumerate(pt.iterchunk(traj, 100)):
c.strip_atoms('!@P')
print(idx, c)
data.append(pt.molsurf(c))
return data
def test_molsurf(self):
traj = self.traj
text = '''
parm {0}
trajin {1}
molsurf @CA
molsurf @CA probe 1.2
molsurf @CA probe 1.2 offset 0.3
'''.format(traj.top.filename, traj.filename)
state = pt.load_cpptraj_state(text)
state.run()
cpp_data = state.data[1:].values
atom_indices = traj.top.select("@CA")
for mask in [atom_indices, '@CA']:
aa_eq(pt.molsurf(traj, mask), cpp_data[0])
aa_eq(pt.molsurf(traj, mask, probe=1.2), cpp_data[1])
aa_eq(pt.molsurf(traj, mask, probe=1.2, offset=0.3), cpp_data[2])
def test_0(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# TrajectoryIterator
aa_eq(pt.molsurf([f.copy() for f in traj], top=traj.top),
pt.molsurf(traj))
# frame_iter
aa_eq(pt.molsurf([f.copy() for f in traj()], top=traj.top),
pt.molsurf(traj))
aa_eq(pt.molsurf([f.copy() for f in traj.iterchunk(3)], top=traj.top),
pt.molsurf(traj))
def test_0(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
# TrajectoryIterator
myiter = WrapBareIterator([f.copy() for f in traj], top=traj.top)
aa_eq(pt.molsurf(myiter), pt.molsurf(traj))
# frame_iter
myiter = WrapBareIterator([f.copy() for f in traj()], top=traj.top)
aa_eq(pt.molsurf(myiter), pt.molsurf(traj))
myiter = WrapBareIterator([f.copy() for f in traj.iterchunk(3)],
top=traj.top)
aa_eq(pt.molsurf(myiter), pt.molsurf(traj))
def test_0(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# TrajectoryIterator
aa_eq(
pt.molsurf([f.copy() for f in traj],
top=traj.top),
pt.molsurf(traj))
# frame_iter
aa_eq(
pt.molsurf([f.copy() for f in traj()],
top=traj.top),
pt.molsurf(traj))
aa_eq(
pt.molsurf([f.copy() for f in traj.iterchunk(3)],
top=traj.top),
pt.molsurf(traj))
import unittest # for travis (you don't need to add this)
# since MD simulations produce huge amount of data (hundreds of GB, few TB
# or enven tens of TB)
# so we always try to use TrajectoryIterator to save memory
# coordinates of specific frames are only loaded if needed
import pytraj as pt
traj = pt.iterload('../tests/data/tz2.ortho.nc',
'../tests/data/tz2.ortho.parm7')
# calculate molsurf for frame 0, 2, 4, 6
# start=0, stop=8, stride=2 (just like python's range(0, 8, 2))
print(pt.molsurf(traj(0, 8, 2), '@CA'))
# if we want to load all frames at once, use [] indexing style
# (just like indexing a list/array in python)
print(pt.molsurf(traj[0:8:2], '@CA'))
# we even perform `autoimage`
print(pt.radgyr(traj(0, 8, 2, autoimage=True), '@CA', nomax=True))
def test_molsurf():
# OK
pt.molsurf(traj(stop=-3, stride=2, autoimage=True, rmsfit=0))
def test(traj=traj):
return pt.molsurf(traj, '@P')
from pytraj.utils.progress import ProgressBarTrajectory
# using pdb file
# traj4 = pt.load("1gwd.v5.cif")
# print("Traj4:")
# print(traj4)
#loading in with iter
traj2 = pt.iterload("heat1.mdcrd", "1gwd.v5.cif")
print("Traj2:")
print(traj2)
#prog = ProgressBarTrajectory(traj2, style='circle')
pt.molsurf(traj2, '@C')
# make changes to file (MATH STUFF HAPPENS!??)
# traj3 = traj2[2:8:2, '!@C=']
# print(traj3.topology())
# print("Changed:")
# print(traj3)
# # saving to new file
# basename = "nickysims.pdb"
def test_molsurf():
# OK
pt.molsurf(traj(stop=-3, stride=2, autoimage=True, rmsfit=0))